CRISPR Journal最新文献_第8页

Widespread Impact of Natural Genetic Variations in CRISPR-Cas9 Outcomes. 自然基因变异对 CRISPR-Cas9 结果的广泛影响。

IF 3.7 4区生物学

CRISPR Journal Pub Date : 2024-10-01 DOI: 10.1089/crispr.2024.0020

Victoria R Li, Tinghui Wu, Alicja Tadych, Aaron Wong, Zijun Zhang

{"title":"Widespread Impact of Natural Genetic Variations in CRISPR-Cas9 Outcomes.","authors":"Victoria R Li, Tinghui Wu, Alicja Tadych, Aaron Wong, Zijun Zhang","doi":"10.1089/crispr.2024.0020","DOIUrl":"10.1089/crispr.2024.0020","url":null,"abstract":"The clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein 9 (Cas9) is a genome editing tool widely used in biological research and clinical therapeutics. Natural human genetic variations, through altering the sequence context of CRISPR-Cas9 target regions, can significantly affect its DNA repair outcomes and ultimately lead to different editing efficiencies. However, these effects have not been systematically studied, even as CRISPR-Cas9 is broadly applied to primary cells and patient samples that harbor such genetic diversity. Here, we present comprehensive investigations of natural genetic variations on CRISPR-Cas9 outcomes across the human genome. The utility of our analysis is illustrated in two case studies, on both preclinical discoveries of CD33 knockout in chimeric antigen receptor-T cell therapy and clinical applications of transthyretin (TTR) inactivation for treating TTR amyloidosis. We further expand our analysis to genome-scale, population-stratified common variants that may lead to gene editing disparity. Our analyses demonstrate pitfalls of failing to account for the widespread genetic variations in Cas9 target selection and how they can be effectively examined and avoided using our method. To facilitate broad access to our analysis, a web platform CROTONdb is developed, which provides predictions for all possible CRISPR-Cas9 target sites in the coding and noncoding regulatory regions, spanning over 5.38 million guide RNA targets and 90.82 million estimated variant effects. We anticipate CROTONdb having broad clinical utilities in gene and cellular therapies.","PeriodicalId":54232,"journal":{"name":"CRISPR Journal","volume":"7 5","pages":"283-292"},"PeriodicalIF":3.7,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142480631","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Challenging the Boundaries Between Treatment, Prevention, and Enhancement in Human Genome Editing. 挑战人类基因组编辑中治疗、预防和增强之间的界限。

IF 3.7 4区生物学

CRISPR Journal Pub Date : 2024-08-01 Epub Date: 2024-07-08 DOI: 10.1089/crispr.2024.0021

Margaret Waltz, Rebecca L Walker, Michael A Flatt, Douglas MacKay, John M Conley, Eric T Juengst, R Jean Cadigan

{"title":"Challenging the Boundaries Between Treatment, Prevention, and Enhancement in Human Genome Editing.","authors":"Margaret Waltz, Rebecca L Walker, Michael A Flatt, Douglas MacKay, John M Conley, Eric T Juengst, R Jean Cadigan","doi":"10.1089/crispr.2024.0021","DOIUrl":"10.1089/crispr.2024.0021","url":null,"abstract":"Traditional distinctions between treatment and enhancement goals for human genome editing (HGE) have animated oversight considerations, yet these categories have been complicated by the addition of prevention as a possible target for HGE applications. To assess the role these three categories might play in continued HGE governance efforts, we report on interviews with genome editing scientists and governance group members. While some accepted traditional distinctions between treatment and enhancement and rejected the latter as unacceptable, others argued that the concept of enhancement is largely irrelevant or not as morally problematic as suggested. Others described how preventive goals for HGE create gray zones where prevention and enhancement may be difficult to distinguish, which may stymie uses of HGE. We conclude by discussing the governance implications of these various understandings of treatment, prevention, and enhancement as HGE research moves beyond the treatment of serious disease to embrace longer range preventive goals.","PeriodicalId":54232,"journal":{"name":"CRISPR Journal","volume":" ","pages":"180-187"},"PeriodicalIF":3.7,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11386990/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141560350","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

AI and SynBio Meet CRISPR Heralding a New Genome Editing Era. 人工智能和 SynBio 与 CRISPR 相遇，预示着一个新的基因组编辑时代的到来。

IF 3.7 4区生物学

CRISPR Journal Pub Date : 2024-08-01 DOI: 10.1089/crispr.2024.0063

Rodolphe Barrangou

引用次数: 0

Prime Editing of Vascular Endothelial Growth Factor Receptor 2 Attenuates Angiogenesis In Vitro. 血管内皮生长因子受体 2 的基因编辑抑制体外血管生成

IF 3.7 4区生物学

CRISPR Journal Pub Date : 2024-08-01 Epub Date: 2024-08-07 DOI: 10.1089/crispr.2024.0019

Gaoen Ma, Hui Qi, Hongwei Deng, Lijun Dong, Qing Zhang, Junkai Ma, Yanhui Yang, Xiaohe Yan, Yajian Duan, Hetian Lei

引用次数: 0

Expanding the Genome-Editing Toolbox with Abyssicoccus albus Cas9 Using a Unique Protospacer Adjacent Motif Sequence. 利用独特的原位相邻位点序列扩展 Abyssicoccus albus Cas9 的基因组编辑工具箱

IF 3.7 4区生物学

CRISPR Journal Pub Date : 2024-08-01 Epub Date: 2024-08-07 DOI: 10.1089/crispr.2024.0013

Akiyoshi Nakamura, Hiroshi Yamamoto, Tsubasa Yano, Reika Hasegawa, Yoichi Makino, Nobutaka Mitsuda, Teruhiko Terakawa, Seiichiro Ito, Shigeo S Sugano

{"title":"Expanding the Genome-Editing Toolbox with Abyssicoccus albus Cas9 Using a Unique Protospacer Adjacent Motif Sequence.","authors":"Akiyoshi Nakamura, Hiroshi Yamamoto, Tsubasa Yano, Reika Hasegawa, Yoichi Makino, Nobutaka Mitsuda, Teruhiko Terakawa, Seiichiro Ito, Shigeo S Sugano","doi":"10.1089/crispr.2024.0013","DOIUrl":"10.1089/crispr.2024.0013","url":null,"abstract":"The genome-editing efficiency of the CRISPR-Cas9 system hinges on the recognition of the protospacer adjacent motif (PAM) sequence, which is essential for Cas9 binding to DNA. The commonly used Streptococcus pyogenes (SpyCas9) targets the 5'-NGG-3' PAM sequence, which does not cover all the potential genomic-editing sites. To expand the toolbox for genome editing, SpyCas9 has been engineered to recognize flexible PAM sequences and Cas9 orthologs have been used to recognize novel PAM sequences. In this study, Abyssicoccus albus Cas9 (AalCas9, 1059 aa), which is smaller than SpyCas9, was found to recognize a unique 5'-NNACR-3' PAM sequence. Modification of the guide RNA sequence improved the efficiency of AalCas9-mediated genome editing in both plant and human cells. Predicted structure-assisted introduction of a point mutation in the putative PAM recognition site shifted the sequence preference of AalCas9. These results provide insights into Cas9 diversity and novel tools for genome editing.","PeriodicalId":54232,"journal":{"name":"CRISPR Journal","volume":" ","pages":"197-209"},"PeriodicalIF":3.7,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141903602","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Viral Delivery of Compact CRISPR-Cas12f for Gene Editing Applications. 用于基因编辑应用的紧凑型 CRISPR-Cas12f 病毒递送。

IF 3.7 4区生物学

CRISPR Journal Pub Date : 2024-06-01 Epub Date: 2024-05-02 DOI: 10.1089/crispr.2024.0010

Allison Sharrar, Zuriah Meacham, Johanna Staples-Ager, Luisa Arake de Tacca, David Rabuka, Trevor Collingwood, Michael Schelle

{"title":"Viral Delivery of Compact CRISPR-Cas12f for Gene Editing Applications.","authors":"Allison Sharrar, Zuriah Meacham, Johanna Staples-Ager, Luisa Arake de Tacca, David Rabuka, Trevor Collingwood, Michael Schelle","doi":"10.1089/crispr.2024.0010","DOIUrl":"10.1089/crispr.2024.0010","url":null,"abstract":"Treating human genetic conditions in vivo requires efficient delivery of the CRISPR gene editing machinery to the affected cells and organs. The gene editing field has seen clinical advances with ex vivo therapies and with in vivo delivery to the liver using lipid nanoparticle technology. Adeno-associated virus (AAV) serotypes have been discovered and engineered to deliver genetic material to nearly every organ in the body. However, the large size of most CRISPR-Cas systems limits packaging into the viral genome and reduces drug development flexibility and manufacturing efficiency. Here, we demonstrate efficient CRISPR gene editing using a miniature CRISPR-Cas12f system with expanded genome targeting packaged into AAV particles. We identified efficient guides for four therapeutic gene targets and encoded the guides and the Cas12f nuclease into a single AAV. We then demonstrate editing in multiple cell lines, patient fibroblasts, and primary hepatocytes. We then screened the cells for off-target editing, demonstrating the safety of the therapeutics. These results represent an important step in applying CRISPR editing to diverse genetic sequences and organs in the body.","PeriodicalId":54232,"journal":{"name":"CRISPR Journal","volume":" ","pages":"150-155"},"PeriodicalIF":3.7,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140864386","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Unveiling Off-Target Mutations in CRISPR Guide RNAs: Implications for Gene Region Specificity. 揭示 CRISPR 引导 RNA 的脱靶突变：对基因区域特异性的影响。

IF 3.7 4区生物学

CRISPR Journal Pub Date : 2024-06-01 DOI: 10.1089/crispr.2024.0002

Ali Mertcan Kose, Ozan Kocadagli, Cihan Taştan, Cagdas Aktan, Onur Mert Ünaldı, Elanur Güzenge, Hamza Emir Erdil

{"title":"Unveiling Off-Target Mutations in CRISPR Guide RNAs: Implications for Gene Region Specificity.","authors":"Ali Mertcan Kose, Ozan Kocadagli, Cihan Taştan, Cagdas Aktan, Onur Mert Ünaldı, Elanur Güzenge, Hamza Emir Erdil","doi":"10.1089/crispr.2024.0002","DOIUrl":"https://doi.org/10.1089/crispr.2024.0002","url":null,"abstract":"The revolutionary CRISPR-Cas9 technology has revolutionized genetic engineering, and it holds immense potential for therapeutic interventions. However, the presence of off-target mutations and mismatch capacity poses significant challenges to its safe and precise implementation. In this study, we explore the implications of off-target effects on critical gene regions, including exons, introns, and intergenic regions. Leveraging a benchmark dataset and using innovative data preprocessing techniques, we have put forth the advantages of categorical encoding over one-hot encoding in training machine learning classifiers. Crucially, we use latent class analysis (LCA) to uncover subclasses within the off-target range, revealing distinct patterns of gene region disruption. Our comprehensive approach not only highlights the critical role of model complexity in CRISPR applications but also offers a transformative off-target scoring procedure based on ML classifiers and LCA. By bridging the gap between traditional target-off scoring and comprehensive model analysis, our study advances the understanding of off-target effects and opens new avenues for precision genome editing in diverse biological contexts. This work represents a crucial step toward ensuring the safety and efficacy of CRISPR-based therapies, underscoring the importance of responsible genetic manipulation for future therapeutic applications.","PeriodicalId":54232,"journal":{"name":"CRISPR Journal","volume":"7 3","pages":"168-178"},"PeriodicalIF":3.7,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141452154","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A Story of Perseverance: An Interview with Matthew Porteus. 坚持不懈的故事：马修-波特斯访谈录

IF 3.7 4区生物学

CRISPR Journal Pub Date : 2024-06-01 DOI: 10.1089/crispr.2024.0043

Matthew H Porteus, Kevin Davies

引用次数: 0

Novel off-Targeting Events Identified after Genome Wide Analysis of CRISPR-Cas Edited Pigs. 对 CRISPR-Cas 编辑过的猪进行全基因组分析后发现的新的非靶向事件。

IF 3.7 4区生物学

CRISPR Journal Pub Date : 2024-06-01 Epub Date: 2024-05-21 DOI: 10.1089/crispr.2024.0012

Bethany K Redel, Junchul Yoon, Emily Reese, Hong An, Kyungjun Uh, Paula R Chen, Randall S Prather, Kiho Lee

{"title":"Novel off-Targeting Events Identified after Genome Wide Analysis of CRISPR-Cas Edited Pigs.","authors":"Bethany K Redel, Junchul Yoon, Emily Reese, Hong An, Kyungjun Uh, Paula R Chen, Randall S Prather, Kiho Lee","doi":"10.1089/crispr.2024.0012","DOIUrl":"10.1089/crispr.2024.0012","url":null,"abstract":"CRISPR-Cas technology has transformed our ability to introduce targeted modifications, allowing unconventional animal models such as pigs to model human diseases and improve its value for food production. The main concern with using the technology is the possibility of introducing unwanted modifications in the genome. In this study, we illustrate a pipeline to comprehensively identify off-targeting events on a global scale in the genome of three different gene-edited pig models. Whole genome sequencing paired with an off-targeting prediction software tool filtered off-targeting events amongst natural variations present in gene-edited pigs. This pipeline confirmed two known off-targeting events in IGH knockout pigs, AR and RBFOX1, and identified other presumably off-targeted loci. Independent validation of the off-targeting events using other gene-edited DNA confirmed two novel off-targeting events in RAG2/IL2RG knockout pig models. This unique strategy offers a novel tool to detect off-targeting events in genetically heterogeneous species after genome editing.","PeriodicalId":54232,"journal":{"name":"CRISPR Journal","volume":" ","pages":"141-149"},"PeriodicalIF":3.7,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11302191/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141072230","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Surveying the State of CRISPR and Gene Editing. 调查 CRISPR 和基因编辑的现状。

IF 3.7 4区生物学

CRISPR Journal Pub Date : 2024-06-01 DOI: 10.1089/crispr.2024.0045

Rodolphe Barrangou

引用次数: 0